Question: 3 years on, continued "Error biexponential transform flowTrans"
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gravatar for dburner1
5 months ago by
dburner10
dburner10 wrote:

When trying to perform biexponential transformation to fluorescence channels in a flowFrame, per Finak et al. BMC Bioinformatics 2010, 11:546, I receive this error:

Error in .Call("flowCore_biexponential_transform", x, a = a, b = b, c = c,  : 
  "flowCore_biexponential_transform" not available for .Call() for package "flowCore"

I see that this error was also reported approximately three years ago ( https://support.bioconductor.org/p/88362/ ) and that a follow-on issue was not fully resolved. I just uninstalled and reinstalled R and all the packages I am using to see if this would help. No change.

My questions are -

  • the original partial fix was to use devtools and install what I take to be modified source on github... but, I am not very computer savvy - I think this will be rabbit hole for me. Is there another way to install the fixed code that is accessible to me, and, if not, what's up (problem was reported ~3 years ago, seems like fix should be in most recent version)?

  • after the person who originally reported this problem used devtools and the source on github, there was a follow-on problem - was this ever fixed/sorted? I assume I may need the fix to the follow-on as well. Follow-on error was -

Error in optim(par = p.ab, mclMultivBiexpAB, y = y, c = p.cd[1], d = p.cd[2],  : 
  L-BFGS-B needs finite values of 'fn

Session info is

R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_New Zealand.1252  LC_CTYPE=English_New Zealand.1252   
[3] LC_MONETARY=English_New Zealand.1252 LC_NUMERIC=C                        
[5] LC_TIME=English_New Zealand.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] flowTrans_1.36.0 flowClust_3.22.0 rmarkdown_1.13   xtable_1.8-4     knitr_1.23      
 [6] shinyBS_0.61     drsmooth_1.9.0   shiny_1.3.2      flowAI_1.14.0    cluster_2.0.9   
[11] fpc_2.2-2        factoextra_1.0.5 ggplot2_3.1.1    flowViz_1.48.0   lattice_0.20-38 
[16] flowCore_1.50.0 

loaded via a namespace (and not attached):
 [1] Biobase_2.44.0      ellipse_0.4.1       assertthat_0.2.1    BiocManager_1.30.4 
 [5] stats4_3.6.0        latticeExtra_0.6-28 robustbase_0.93-5   ggrepel_0.8.1      
 [9] pillar_1.4.1        glue_1.3.1          digest_0.6.19       RColorBrewer_1.1-2 
[13] promises_1.0.1      colorspace_1.4-1    htmltools_0.3.6     httpuv_1.5.1       
[17] plyr_1.8.4          pcaPP_1.9-73        pkgconfig_2.0.2     purrr_0.3.2        
[21] corpcor_1.6.9       mvtnorm_1.0-10      scales_1.0.0        later_0.8.0        
[25] tibble_2.1.3        withr_2.1.2         nnet_7.3-12         BiocGenerics_0.30.0
[29] hexbin_1.27.3       lazyeval_0.2.2      mnormt_1.5-5        magrittr_1.5       
[33] crayon_1.3.4        IDPmisc_1.1.19      mime_0.6            mclust_5.4.3       
[37] evaluate_0.14       MASS_7.3-51.4       changepoint_2.2.2   class_7.3-15       
[41] graph_1.62.0        tools_3.6.0         matrixStats_0.54.0  stringr_1.4.0      
[45] kernlab_0.9-27      munsell_0.5.0       compiler_3.6.0      rlang_0.3.4        
[49] grid_3.6.0          gtable_0.3.0        flexmix_2.3-15      reshape2_1.4.3     
[53] rrcov_1.4-7         R6_2.4.0            zoo_1.8-6           prabclus_2.3-1     
[57] dplyr_0.8.1         clue_0.3-57         KernSmooth_2.23-15  modeltools_0.2-22  
[61] stringi_1.4.3       parallel_3.6.0      Rcpp_1.0.1          DEoptimR_1.0-8     
[65] tidyselect_0.2.5    xfun_0.7            diptest_0.75-7
software error • 104 views
ADD COMMENTlink written 5 months ago by dburner10
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